comparison deepTools_macros.xml @ 13:b4c5dd45778a draft

Uploaded

12:aea72b24dea0

<macros>
    <macro name="bamCorrelate_mode_actions">
        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>

                    help="If not specified the value is set automatically."/>

                <expand macro="colormap" />
            </when>
        </conditional>
    </macro>
    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <macro name="requirements">
        <requirements>
            <requirement type="package" >samtools</requirement>
            <requirement type="package" >deepTools</requirement>
            <requirement type="package" >ucsc_tools</requirement>
            <requirement type="package" version="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49">deepTools</requirement>
            <requirement type="package" version="0.1">ucsc_tools</requirement>
            <requirement type="package" version="1.7.1">numpy</requirement>
            <requirement type="package" version="0.7.7">pysam</requirement>
            <requirement type="package" version="0.12.0">scipy</requirement>
            <requirement type="package" version="1.2.1">matplotlib</requirement>
            <requirement type="package" version="0.1.19">samtools</requirement>
            <requirement type="package" version="12-2013">bx-python</requirement>
            <yield />
        </requirements>
    </macro>
    <macro name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <exit_code range="0" level="warning" description="Warning" />
            <regex match="Error:" />
            <regex match="Exception:" />
            <regex match="EXception:" />
            <regex match="Traceback" />
        </stdio>
    </macro>
    <token name="@REFERENCES@">

For more informations, please visit our `project site`_.

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _project site: https://github.com/fidelram/deepTools

    </token>

    <macro name="multiple_input_bams">
        <repeat name="input_files" title="BAM files" min="2">
            <param name="bamfile" type="data" format="bam" 
                label="Bam file" 
                help="The BAM file must be sorted."/>
            <param name="label" type="text" size="30" optional="true" value=""
                label="Label"
                help="Label to use in the output. If not given the dataset name will be used instead."/>
          </repeat>
    </macro>

    <token name="@multiple_input_bams@">
        #for $i in $input_files:
            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
            #set $temp_input_path = $temp_input_handle.name

                #set $labels += ["\"%s\"" % ($i.bamfile.name)]
            #end if
        #end for
    </token>

    <macro name="reference_genome_source">
        <conditional name="source">
            <param name="ref_source" type="select" label="Reference genome">
                <option value="cached">locally cached</option>
                <option value="history">in your history</option>
            </param>

            </when>
            <when value="history">
                <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
            </when>
        </conditional>
    </macro>

    <token name="@reference_genome_source@">
    #if $source.ref_source=="history":
        --genome $source.input1
    #else:
        --genome "${source.input1_2bit.fields.path}"
    #end if
    </token>

    <macro name="effectiveGenomeSize">
        <conditional name="effectiveGenomeSize">
            <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 
                    Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. 
                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">

            </param>
            <when value="specific">
                <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
            </when>
        </conditional>
    </macro>

    <macro name="image_file_format">
        <param name="outFileFormat" type="select" label="Image file format">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="eps">eps</option>
            <option value="emf">emf</option>
        </param>
    </macro>

    <macro name="graphic_output_settings">
        <conditional name="output" >
            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <yield />
                <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
                <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
            </when>
        </conditional>
    </macro>

    <macro name="input_image_file_format">
        <param name="outFileFormat" type="select" label="Image file format">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="eps">eps</option>
            <option value="emf">emf</option>
        </param>
    </macro>

    <macro name="output_image_file_format">
        <data format="png" name="outFileName" label="${tool.name} image">
            <change_format>
                <when input="output.outFileFormat" value="pdf" format="pdf" />
                <when input="output.outFileFormat" value="svg" format="svg" />
                <when input="output.outFileFormat" value="eps" format="eps" />
                <when input="output.outFileFormat" value="emf" format="emf" />
            </change_format>
        </data>
    </macro>

    <macro name="output_graphic_outputs">
        <yield />
        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveData'] is True
            ))
            </filter>
        </data>
        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveMatrix'] is True
            ))
            </filter>
        </data>
        <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
            <filter>

                output['showOutputSettings'] == 'yes' and 
                output['saveSortedRegions'] is True
            ))
            </filter>
        </data>
    </macro>

    <macro name="colormap">
        <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
            <option value="RdYlBu" selected="true">RdYlBu</option>
            <option value="Accent">Accent</option>
            <option value="Spectral">Spectral</option>
            <option value="Set1">Set1</option>

            <option value="brg_r">brg reversed</option>
            <option value="jet_r">jet reversed</option>
            <option value="afmhot_r">afmhot reversed</option>
        </param>

    </macro>

</macros>

13:b4c5dd45778a

<macros>
    <xml name="bamCorrelate_mode_actions">
        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>

                    help="If not specified the value is set automatically."/>

                <expand macro="colormap" />
            </when>
        </conditional>
    </xml>
    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" >samtools</requirement>
            <requirement type="package" >deepTools</requirement>
            <requirement type="package" >ucsc_tools</requirement>
            <requirement type="package" version="1.5.4_74aac0843a956ca352e3e85087f20c8f158e2f7d">deepTools</requirement>
            <requirement type="package" version="0.1">ucsc_tools</requirement>
            <requirement type="package" version="1.7.1">numpy</requirement>
            <requirement type="package" version="0.7.7">pysam</requirement>
            <requirement type="package" version="0.12.0">scipy</requirement>
            <requirement type="package" version="1.2.1">matplotlib</requirement>
            <requirement type="package" version="0.1.19">samtools</requirement>
            <requirement type="package" version="12-2013">bx-python</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
            <regex match="EXception:" />
            <regex match="Traceback" />
        </stdio>
    </xml>
    <token name="@REFERENCES@">

For more informations, please visit our `project site`_.

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _project site: https://github.com/fidelram/deepTools

    </token>

    <xml name="multiple_input_bams">
        <repeat name="input_files" title="BAM files" min="2">
            <param name="bamfile" type="data" format="bam" 
                label="Bam file" 
                help="The BAM file must be sorted."/>
            <param name="label" type="text" size="30" optional="true" value=""
                label="Label"
                help="Label to use in the output. If not given the dataset name will be used instead."/>
          </repeat>
    </xml>

    <token name="@multiple_input_bams@">
        #for $i in $input_files:
            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
            #set $temp_input_path = $temp_input_handle.name

                #set $labels += ["\"%s\"" % ($i.bamfile.name)]
            #end if
        #end for
    </token>

    <xml name="reference_genome_source">
        <conditional name="source">
            <param name="ref_source" type="select" label="Reference genome">
                <option value="cached">locally cached</option>
                <option value="history">in your history</option>
            </param>

            </when>
            <when value="history">
                <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
            </when>
        </conditional>
    </xml>

    <token name="@reference_genome_source@">
    #if $source.ref_source=="history":
        --genome $source.input1
    #else:
        --genome "${source.input1_2bit.fields.path}"
    #end if
    </token>

    <xml name="effectiveGenomeSize">
        <conditional name="effectiveGenomeSize">
            <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 
                    Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. 
                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">

            </param>
            <when value="specific">
                <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
            </when>
        </conditional>
    </xml>

    <xml name="image_file_format">
        <param name="outFileFormat" type="select" label="Image file format">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="eps">eps</option>
            <option value="emf">emf</option>
        </param>
    </xml>

    <xml name="input_save_matrix_values">
        <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
    </xml>

    <xml name="input_graphic_output_settings">
        <conditional name="output" >
            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <yield />
                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
            </when>
        </conditional>
    </xml>

    <xml name="input_image_file_format">
        <param name="outFileFormat" type="select" label="Image file format">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="eps">eps</option>
            <option value="emf">emf</option>
        </param>
    </xml>

    <xml name="output_image_file_format">
        <data format="png" name="outFileName" label="${tool.name} image">
            <change_format>
                <when input="output.outFileFormat" value="pdf" format="pdf" />
                <when input="output.outFileFormat" value="svg" format="svg" />
                <when input="output.outFileFormat" value="eps" format="eps" />
                <when input="output.outFileFormat" value="emf" format="emf" />
            </change_format>
        </data>
    </xml>

    <xml name="output_save_matrix_values">
        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveMatrix'] is True
            ))
            </filter>
        </data>
    </xml>

    <xml name="output_graphic_outputs">
        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveData'] is True
            ))
            </filter>
        </data>
        <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
            <filter>

                output['showOutputSettings'] == 'yes' and 
                output['saveSortedRegions'] is True
            ))
            </filter>
        </data>
    </xml>

    <xml name="colormap">
        <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
            <option value="RdYlBu" selected="true">RdYlBu</option>
            <option value="Accent">Accent</option>
            <option value="Spectral">Spectral</option>
            <option value="Set1">Set1</option>

            <option value="brg_r">brg reversed</option>
            <option value="jet_r">jet reversed</option>
            <option value="afmhot_r">afmhot reversed</option>
        </param>

    </xml>

</macros>